fix getGenotypedCaller issue

nf-cmgg · Mar 1, 2024 · 5764904 · 5764904
1 parent 27f6d0f
commit 5764904
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Showing 8 changed files with 98 additions and 106 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -10,14 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-def getGenotypedCaller(caller) {
-    def output = caller
-    if(caller == "haplotypecaller") {
-        output = "gatk4-joint"
-    }
-    return output
-}
-
 def enableOutput(state) {
     """
     This function checks if the output of the given module should be published to the output directory.
@@ -40,11 +32,11 @@ def final_output = { "${params.outdir}/${params.project ? "${date}_${params.proj
 def final_output_reports = { "${params.outdir}/${params.project ? "${date}_${params.project}" : "${date}_${workflow.runName}"}/${meta.family}/reports" }
 def individual_output = { "${params.outdir}/${meta.sample}" }
 def individual_reports = { "${params.outdir}/${meta.sample}/reports" }
-def individual_validation = { "${params.outdir}/${meta.sample}/validation/${getGenotypedCaller(meta.caller)}" }
+def individual_validation = { "${params.outdir}/${meta.sample}/validation/${meta.caller}" }
 
 def callers = params.callers.tokenize(",")
 
-def final_prefix = params.output_suffix ? { "${meta.id}${params.output_suffix}" } : { "${meta.id}.${getGenotypedCaller(meta.caller)}" }
+def final_prefix = params.output_suffix ? { "${meta.id}${params.output_suffix}" } : { "${meta.id}.${meta.caller}" }
 
 process {
 

diff --git a/tests/annotate_test.nf.test b/tests/annotate_test.nf.test
@@ -18,11 +18,11 @@ nextflow_pipeline {
             def date = new java.text.SimpleDateFormat("yyyy-MM-dd").format(new Date())
             assertAll {
                 assert workflow.success
-                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.gatk4-joint.bcftools_stats.txt").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.gatk4-joint.somalier.html").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.vcf.gz").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.vcf.gz.tbi").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.ped").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.haplotypecaller.bcftools_stats.txt").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.haplotypecaller.somalier.html").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.vcf.gz").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.vcf.gz.tbi").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.ped").exists()
                 assert file("${outputDir}/${date}_test/Proband_12345/reports/DNA049572.vardict.bcftools_stats.txt").exists()
                 assert file("${outputDir}/${date}_test/Proband_12345/reports/NA24385D2_NVQ_034.vardict.bcftools_stats.txt").exists()
                 assert file("${outputDir}/${date}_test/Proband_12345/reports/DNA049572.vardict.somalier.html").exists()

diff --git a/tests/filter_test.nf.test b/tests/filter_test.nf.test
@@ -17,10 +17,10 @@ nextflow_pipeline {
             def date = new java.text.SimpleDateFormat("yyyy-MM-dd").format(new Date())
             assertAll {
                 assert workflow.success
-                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.gatk4-joint.bcftools_stats.txt").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.gatk4-joint.somalier.html").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.vcf.gz").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.ped").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.haplotypecaller.bcftools_stats.txt").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.haplotypecaller.somalier.html").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.vcf.gz").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.ped").exists()
                 assert file("${outputDir}/${date}_test/Proband_12345/reports/DNA049572.vardict.bcftools_stats.txt").exists()
                 assert file("${outputDir}/${date}_test/Proband_12345/reports/NA24385D2_NVQ_034.vardict.bcftools_stats.txt").exists()
                 assert file("${outputDir}/${date}_test/Proband_12345/reports/DNA049572.vardict.somalier.html").exists()

diff --git a/tests/full_gvcf.nf.test b/tests/full_gvcf.nf.test
@@ -28,34 +28,34 @@ nextflow_pipeline {
             def date = new java.text.SimpleDateFormat("yyyy-MM-dd").format(new Date())
             assertAll {
                 assert workflow.success
-                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.gatk4-joint.bcftools_stats.txt").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.gatk4-joint.somalier.html").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.vcf.gz").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.vcf.gz.tbi").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.ped").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.ped").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.db").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.haplotypecaller.bcftools_stats.txt").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.haplotypecaller.somalier.html").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.vcf.gz").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.vcf.gz.tbi").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.ped").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.ped").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.db").exists()
                 assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.bed").exists()
                 assert file("${outputDir}/multiqc/multiqc_report.html").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.fn.vcf.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.fn.vcf.gz.tbi").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.fp.vcf.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.fp.vcf.gz.tbi").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.non_snp_roc.tsv.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.phasing.txt").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.non_snp.png").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.non_snp.svg").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.snp.png").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.snp.svg").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.weighted.png").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.weighted.svg").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.snp_roc.tsv.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.summary.txt").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.tp-baseline.vcf.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.tp-baseline.vcf.gz.tbi").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.tp.vcf.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.tp.vcf.gz.tbi").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.weighted_roc.tsv.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.fn.vcf.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.fn.vcf.gz.tbi").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.fp.vcf.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.fp.vcf.gz.tbi").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.non_snp_roc.tsv.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.phasing.txt").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.non_snp.png").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.non_snp.svg").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.snp.png").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.snp.svg").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.weighted.png").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.weighted.svg").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.snp_roc.tsv.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.summary.txt").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.tp-baseline.vcf.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.tp-baseline.vcf.gz.tbi").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.tp.vcf.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.tp.vcf.gz.tbi").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.weighted_roc.tsv.gz").exists()
             }
         }
 

diff --git a/tests/full_wes.nf.test b/tests/full_wes.nf.test
@@ -27,12 +27,12 @@ nextflow_pipeline {
             def date = new java.text.SimpleDateFormat("yyyy-MM-dd").format(new Date())
             assertAll {
                 assert workflow.success
-                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.gatk4-joint.bcftools_stats.txt").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.gatk4-joint.somalier.html").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.vcf.gz").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.vcf.gz.tbi").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.ped").exists()
-                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.gatk4-joint.db").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.haplotypecaller.bcftools_stats.txt").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/reports/Proband_12345.haplotypecaller.somalier.html").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.vcf.gz").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.vcf.gz.tbi").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.ped").exists()
+                assert file("${outputDir}/${date}_test/Proband_12345/Proband_12345.haplotypecaller.db").exists()
                 assert file("${outputDir}/${date}_test/Proband_12345/reports/DNA049572.vardict.bcftools_stats.txt").exists()
                 assert file("${outputDir}/${date}_test/Proband_12345/reports/NA24385D2_NVQ_034.vardict.bcftools_stats.txt").exists()
                 assert file("${outputDir}/${date}_test/Proband_12345/reports/DNA049572.vardict.somalier.html").exists()
@@ -55,25 +55,25 @@ nextflow_pipeline {
                 assert file("${outputDir}/DNA049572/DNA049572.haplotypecaller.g.vcf.gz.tbi").exists()
                 assert file("${outputDir}/DNA049572/DNA049572.bed").exists()
                 assert file("${outputDir}/multiqc/multiqc_report.html").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.fn.vcf.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.fn.vcf.gz.tbi").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.fp.vcf.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.fp.vcf.gz.tbi").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.non_snp_roc.tsv.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.phasing.txt").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.non_snp.png").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.non_snp.svg").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.snp.png").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.snp.svg").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.weighted.png").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.weighted.svg").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.snp_roc.tsv.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.summary.txt").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.tp-baseline.vcf.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.tp-baseline.vcf.gz.tbi").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.tp.vcf.gz").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.tp.vcf.gz.tbi").exists()
-                assert file("${outputDir}/DNA049572/validation/gatk4-joint/DNA049572.weighted_roc.tsv.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.fn.vcf.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.fn.vcf.gz.tbi").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.fp.vcf.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.fp.vcf.gz.tbi").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.non_snp_roc.tsv.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.phasing.txt").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.non_snp.png").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.non_snp.svg").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.snp.png").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.snp.svg").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.weighted.png").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.weighted.svg").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.snp_roc.tsv.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.summary.txt").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.tp-baseline.vcf.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.tp-baseline.vcf.gz.tbi").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.tp.vcf.gz").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.tp.vcf.gz.tbi").exists()
+                assert file("${outputDir}/DNA049572/validation/haplotypecaller/DNA049572.weighted_roc.tsv.gz").exists()
                 assert file("${outputDir}/DNA049572/validation/vardict/DNA049572.fn.vcf.gz").exists()
                 assert file("${outputDir}/DNA049572/validation/vardict/DNA049572.fn.vcf.gz.tbi").exists()
                 assert file("${outputDir}/DNA049572/validation/vardict/DNA049572.fp.vcf.gz").exists()